The Complete Plastome Sequences of Four Orchid Species: Insights into the Evolution of the Orchidaceae and the Utility of Plastomic Mutational Hotspots

Abstract

Orchidaceae (orchids) is the largest family in the monocots, including about 25,000 species in 880 genera and five subfamilies. Many orchids are highly valued for their beautiful and long-lasting flowers. However, the phylogenetic relationships among the five orchid subfamilies remain unresolved. The major dispute centers on whether the three one-stamened subfamilies, Epidendroideae, Orchidoideae, and Vanilloideae, are monophyletic or paraphyletic. Moreover, structural changes in the plastid genome (plastome) and the effective genetic loci at the species-level phylogenetics of orchids have rarely been documented. In this study, we compared 53 orchid plastomes, including four newly sequenced ones, that represent four remote genera: Dendrobium, Goodyera, Paphiopedilum, and Vanilla. These differ from one another not only in their lengths of inverted repeats and small single copy regions but also in their retention of ndh genes. Comparative analyses of the plastomes revealed that the expansion of inverted repeats in Paphiopedilum and Vanilla is associated with a loss of ndh genes. In orchid plastomes, mutational hotspots are genus specific. After having carefully examined the data, we propose that the three loci 5′trnK-rps16, trnS-trnG, and rps16-trnQ might be powerful markers for genera within Epidendroideae, and clpP-psbB and rps16-trnQ might be markers for genera within Cypripedioideae. After analyses of a partitioned dataset, we found that our plastid phylogenomic trees were congruent in a topology where two one-stamened subfamilies (i.e., Epidendroideae and Orchidoideae) were sisters to a multi-stamened subfamily (i.e., Cypripedioideae) rather than to the other one-stamened subfamily (Vanilloideae), suggesting that the living one-stamened orchids are paraphyletic.

Plastome Evolution and Phylogeny of Orchidaceae, With 24 New Sequences

“…Similar gene rearrangement events within a plastome have been reported in Campanulaceae (Cosner et al, 1997), conifers (Hirao et al, 2008), Fabaceae (Cai et al, 2008), Geraniaceae (Chumley et al, 2006), and Oleaceae (Lee et al, 2007). Contractions of the small single copy (SSC) region similar to that of Geraniaceae were also reported in Paphiopedilum (Kim et al, 2015a;Niu et al, 2017b;Hou et al, 2018) and Vanilla (Lin et al, 2015;Amiryousefi et al, 2017).…”

“…Phylogenetic studies of Orchidaceae using entire plastomes are in a relatively early stage because of limited available plastome sequences (Givnish et al, 2015;Kim et al, 2015a;Lin et al, 2015;Niu et al, 2017b;Dong et al, 2018). But the relationships among major orchid lineages determined using whole plastomes agree well to the large-scale phylogenetic studies of Orchidaceae using two or three genes (Górniak et al, 2010;Freudenstein and Chase, 2015).…”

“…Although the loss or pseudogenization of ndh genes was also observed in terrestrial taxonomic groups (Apostasia, Calypso, Cephalanthera, Cremastra, Cymbidium, Epipactis, Goodyera, Kuhlhasseltia, Limodorum, Liparis, Neuwiedia, Oncidium, Paphiopedilum, Phragmipedium, Platanthera, and Pogonia), the frequencies are low compared to epiphytes. Although the loss or pseudogenization of ccsA, cemA, and infA is often observed in addition to ndh gene non-functionalization, but no clear trend has been found (Barrett et al, 2014;Kim et al, 2015a;Feng et al, 2016;Niu et al, 2017b;Hou et al, 2018). In the phylogenetic tree, the non-functionalization of ndh appears to occur gradually and independently in the process of pseudogenization in many independent lineages ( Figure 6).…”

“…; and Neottia, 7 spp.) in which at least five plastomes per genus have been decoded (Logacheva et al, 2011;Barrett and Davis, 2012;Yang et al, 2013;Barrett et al, 2014;Feng et al, 2016;Niu et al, 2017b;Kim et al, 2018). Among them, Corallorhiza and Neottia have been subjected to extensive evolutionary studies of their plastomes because both photosynthetic and nonphotosynthetic species occur in a congeneric group (Barrett and Davis, 2012;Barrett et al, 2014;Feng et al, 2016;.…”

“…For examples, extensive gene losses have been reported in several independent mycoheterotrophic orchid lineages-i.e., Aphyllorchis (Feng et al, 2016), Cyrtosia (Kim et al, 2019), Epipogium (Schelkunov et al, 2015), Gastrodia (Yuan et al, 2018), Hexalectris (Barrett and Kennedy, 2018) and Rhizanthella (Delannoy et al, 2011). In addition, ndh deletion and pseudogenization are assumed to be phenomena that occur independently in many orchid lineages such as Apostasia (Lin et al, 2017;Niu et al, 2017a), Calypso , Cattleya (da Rocha Perini et al, 2016), Cephalanthera (Feng et al, 2016), Cremastra (Dong et al, 2018), Cymbidium (Yang et al, 2013;Kim et al, 2018;Wang et al, 2018), Dendrobium (Niu et al, 2017b), Epipactis (Dong et al, 2018), Eulophia (Huo et al, 2017), Holcoglossum (Li et al, 2019), Limodorum (Lallemand et al, 2019), Liparis (Krawczyk et al, 2018), Neuwiedia (Niu et al, 2017a), Oncidium (Wu et al, 2010;Kim et al, 2015a), Paphiopedilum (Niu et al, 2017b;Hou et al, 2018), Phalaenopsis (Chang et al, 2006), Phragmipedium (Kim et al, 2015a), Platanthera (Dong et al, 2018), Vanilla (Lin et al, 2015), and Vanda (Li et al, 2019). On the other hand, full ndh genes have been reported in members of Anoectochilus (Yu et al, 2016), Calanthe (Dong et al, 2018), Cypripedium (Kim et al, 2015b;Lin et al, 2015), Habenaria…”